STARD3 p.Phe59=
c.177C>T · rs150342077 · VCV2647718
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.04%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -4.4 |
| Overall | ||
| CADD | 13.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.04%
Middle Eastern · 63/6,062 alleles
Filtering AF
0.834%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.759%
Overall
0.11%
1,773/1,614,220 alleles · low-frequency
exomes 1,614/1,461,846 · genomes 159/152,374 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.04% | 96 |
| Ashkenazi Jewishnot grpmax-eligible | 0.297% | 336 |
| South Asian | 0.233% | 430 |
| Remaining individualsnot grpmax-eligible | 0.182% | 548 |
| Admixed American | 0.108% | 924 |
| European (non-Finnish) | 0.103% | 973 |
| African / African-American | 0.0173% | 5,775 |
| Finnishnot grpmax-eligible | 0.00469% | 21,339 |
| East Asian | 0.00446% | 22,443 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- STARD3
- Protein
- p.Phe59=
- Coding
- c.177C>T
- MANE Select
- NM_006804
- dbSNP
- rs150342077
- Type
- single nucleotide variant
- Location
- chr17:39653708 (GRCh38)
- Gene constraint
- LOEUF 0.812 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.09 · 5 PDB
- Residue 59
- the mental domain
Similar variants
- STARD3 p.Ala187Thr Uncertain significance ★ ⚠ same type
- STARD3 p.Ala293Val Uncertain significance ★ ⚠ same type
- STARD3 p.Ala394Ser Uncertain significance ★ ⚠ same type
- STARD3 p.Ala443Ser Uncertain significance ★ ⚠ same type
- STARD3 p.Arg105Cys Uncertain significance ★ ⚠ same type
- STARD3 p.Arg14Gly Uncertain significance ★ ⚠ same type
- STARD3 p.Arg14His Uncertain significance ★ ⚠ same type
- STARD3 p.Arg193Cys Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/stard3-p-phe59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown